Comparative Study of Time-Dependent Aluminum Exposure and Post-Exposure Recovery Shows Better Improvement in Synaptic Changes and Neuronal Pathology in Rat Brain After Short-Term Exposure

Aluminum is a ubiquitous metal that causes multiple brain pathologies such as, cognitive dysfunction and Alzheimer's disease like symptoms. Exposure to aluminum through drinking water is responsible for hampering learning and memory. This study aimed to compare (1) the time-dependent effect of aluminum exposure (keeping total exposure of 5850 mg/kg same) in two durations, 30 and 45 days, and (2) to compare post-exposure self-recovery effect after 20 days in both (30 and 45 days exposure) groups. Rats were given 130 and 195 mg/kg of AlCl₃·6H₂O for 45 and 30 days respectively, to see the time-dependent exposure effect. At the end of exposure, rats were given distilled water and allowed to self-recover for 20 days to study the recovery. Expression levels of synaptic genes (Syp, SNAP25, Nrxn1/2, PSD95, Shank1/2, Homer1, CamkIV, Nrg1/2 and Kalrn) were measured using qPCR and compared in the exposure and recovery groups. Cellular morphology of the rat brain cortex and hippocampus was also investigated. Damage in lipid and protein profile was measured by employing FTIR. Results showed downregulation of mRNA expression of synaptic genes, plaques deposition, disorganization in lipid and protein profile by increasing membrane fluidity, and disorder and alteration of protein secondary structure after both exposure periods. However, better improvement/recovery in these parameters were observed in recovery group of 30 days aluminum exposure compared to 45 days aluminum exposure group. Taken together, these results suggested that short-term exposure resulted in better restoration of lipid and protein profile after time-dependent exposure of aluminum than prolonged exposure.

Persistent white matter vulnerability in a mouse model of mild traumatic brain injury

Background

Following one mild traumatic brain injury (mTBI), there is a window of vulnerability during which subsequent mTBIs can cause substantially exacerbated impairments. Currently, there are no known methods to monitor, shorten or mitigate this window.

Methods

To characterize a preclinical model of this window of vulnerability, we first gave male and female mice one or two high-depth or low-depth mTBIs separated by 1, 7, or 14 days. We assessed brain white matter integrity using silver staining within the corpus callosum and optic tracts, as well as behavioural performance on the Y-maze test and visual cliff test.

Results

The injuries resulted in windows of white matter vulnerability longer than 2 weeks but produced no behavioural impairments. Notably, this window duration is substantially longer than those reported in any previous preclinical vulnerability study, despite our injury model likely being milder than the ones used in those studies. We also found that sex and impact depth differentially influenced white matter integrity in different white matter regions.

Conclusions

These results suggest that the experimental window of vulnerability following mTBI may be longer than previously reported. Additionally, this work highlights the value of including white matter damage, sex, and replicable injury models for the study of post-mTBI vulnerability and establishes important groundwork for the investigation of potential vulnerability mechanisms, biomarkers, and therapies.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12868-022-00730-y.

Time Course of Remote Neuropathology Following Diffuse Traumatic Brain Injury in the Male Rat

Traumatic brain injury (TBI) can affect different regions throughout the brain. Regions near the site of impact are the most vulnerable to injury. However, damage to distal regions occurs. We investigated progressive neuropathology in the dorsal hippocampus (near the impact) and cerebellum (distal to the impact) after diffuse TBI. Adult male rats were subjected to midline fluid percussion injury or sham injury. Brain tissue was stained by the amino cupric silver stain. Neuropathology was quantified in sub-regions of the dorsal hippocampus at 1, 7, and 28 days post-injury (DPI) and coronal cerebellar sections at 1, 2, and 7 DPI. The highest observed neuropathology in the dentate gyrus occurred at 7 DPI which attenuated by 28 DPI, whereas the highest observed neuropathology was at 1 DPI in the CA3 region. There was no significant neuropathology in the CA1 region at any time point. Neuropathology was increased at 7 DPI in the cerebellum compared to shams and stripes of pathology were observed in the molecular layer perpendicular to the cerebellar cortical surface. Together these data show that diffuse TBI can result in neuropathology across the brain. By describing the time course of pathology in response to TBI, it is possible to build the temporal profile of disease progression.

Novel SOD1 monoclonal antibodies against the electrostatic loop preferentially detect misfolded SOD1 aggregates

Amyotrophic lateral sclerosis (ALS) is a progressive neurological disease that leads to motor neuron degeneration and paralysis. Superoxide dismutase (SOD1) mutations are the second most common cause of familial ALS and are responsible for up to 20 % of familial ALS cases. In ALS patients, SOD1 can form toxic misfolded aggregates that deposit in the brain and spinal cord. To better detect SOD1 aggregates and expand the repertoire of conformational SOD1 antibodies, SOD1 monoclonal antibodies were generated by immunizing SOD1 knockout mice with an SOD1 fragment consisting of amino acids 129-146, which make up part of the electrostatic loop. A series of hybridomas secreting antibodies were screened and five different SOD1 monoclonal antibodies (2C10, 2F8, 4B11, 5H5, and 5A10) were found to preferentially detect denatured or aggregated SOD1 by enzyme-linked immunosorbent assay (ELISA), filter trap assay, and immunohistochemical analysis in SOD1 mouse models. The staining with these antibodies was compared to Campbell-Switzer argyrophilic reactivity of pathological inclusions. These new conformational selective SOD1 antibodies will be useful for clinical diagnosis of SOD1 ALS and potentially for passive immunotherapy.

Re-evaluation of the 18 non-human protein standards used to create the empirical statistical model for decoy library searching

The Empirical Statistical Model (ESM) for decoy library searching fused the expected amino acid sequence of 18 non-human protein standards to a human decoy library. The ESM assumed a priori the standards were pure such that only the 18 nominal proteins were true positive, all other proteins were false positive, there was no overlap in the peptides of non-human proteins versus human proteins, and that the score distribution of individual peptides would resolve true positive from false positive results or noise. The results of random and independent sampling by LC-ESI-MS/MS indicated that the fundamental assumptions of the ESM were not in good agreement with the actual purity of the commercial test standards and so the method showed a 99.7% false negative rate. The ESM for decoy library searching apparently showed poor agreement with SDS-PAGE using silver staining, goodness of fit of MS/MS spectra by X!TANDEM, FDR correction by Benjamini and Hochberg, or comparison to the observation frequency of null random MS/MS spectra, that all confirmed the standards contain hundreds of proteins with a low FDR of primary structural identification. The protein observation frequency increased with abundance and the log₁₀ precursor intensity distributions were Gaussian and nearly ideal for relative quantification.

A multiple signal amplification sandwich-type SERS biosensor for femtomolar detection of miRNA

MicroRNAs are widely used as tumor markers for cancer diagnosis and prognosis. Herein, a multiple signal amplification sandwich-type SERS biosensor for femtomolar detection of miRNA is reported. The signal unit consisted of giant Au vesicles, DNA sequences and deposited silver nanoparticles. The giant Au vesicles provided large-volume hot spots because of sharp tips and abundant hotspot gaps, thus enhancing the electromagnetic intensity for the SERS performance. Further silver stain would easily lead to second-stage amplification of Raman signal. In addition, more SERS signal molecules R6G adsorbed on the signal unit with the aid of HCR and the controlled nanogaps between adjacent AgNPs, brought about the third-stage amplification. The capture unit, prepared by immobilizing the capture probe (CP) on the Fe₃O₄@AuNPs, could easily capture target miRNA and greatly simplify the separation step to improve reproducibility. The higher concentration of target miRNA definitely formed more sandwich-type structures with combination of capture unit and signal unit, resulting in multiple amplification of SERS signals. The proposed multiple signal amplification sandwich-type SERS biosensor could detect miRNA-141 at the femtomolar level with a low detection limit of 0.03 fM. Meanwhile, it exhibited high selectivity and accuracy, even for practical analysis in human serum. Therefore, the designed multiple signal amplification sandwich-type SERS biosensor would be a very promising alternative tool for the detection of miRNA and analogs in the field of biomedical diagnosis.

Protocol for the Analysis of Laser Capture Microdissected Fresh-Frozen Tissue Homogenates by Silver-Stained 1D SDS-PAGE

The heterogeneity present in solid tumors adds significant difficulty to scientific analysis and improved understanding. Fundamentally, solid tumor formation consists of cancer cells proper along with stromal elements. The burgeoning malignant process is dependent upon modified stromal elements. Collectively, the stroma forms an essential microenvironment, which is indispensable for the survival and growth of the malignant neoplasm. This cellular heterogeneity makes molecular profiling of solid tumors via mass spectrometry (MS)-based proteomics a daunting task. Laser capture microdissection (LCM) is commonly used to obtain distinct histological cell types (e.g., tumor parenchymal cells, stromal cells) from tumor tissue and attempt to address the tumor heterogeneity interference with downstream liquid chromatography (LC) MS analysis. To provide optimal LC-MS analysis of micro-scale and/or nano-scale tissue sections, we modified and optimized a silver-stained one-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (1D-SDS-PAGE) protocol for the LC-MS analysis of LCM-procured fresh-frozen tissue specimens. Presented is a detailed in-gel digestion protocol adjusted specifically to maximize the proteome coverage of amount-limited LCM samples, and facilitate in-depth molecular profiling. Following LCM, targeted tissue sections are further fractionated using silver-stained 1D-SDS-PAGE to resolve and visualize tissue proteins prior to in-gel digestion and subsequent LC-MS analysis.

Detection and Quantification of Protein Aggregates in Plants

Plants are constantly exposed to a complex and changing environment that challenges their cellular homeostasis. Stress responses triggered as a consequence of unfavorable conditions result in increased protein aggregate formation at the cellular level. When the formation of misfolded proteins surpasses the capacity of the cell to remove them, insoluble protein aggregates accumulate. In the animal field, an enormous effort is being placed to uncover the mechanisms regulating aggregate formation because of its implications in many important human diseases. Because of its importance for cellular functionality and fitness, it is equally important to expand plant research in this field. Here, we describe a cell fractionation-based method to obtain very pure insoluble protein aggregate fractions that can be subsequently semiquantified using image analysis. This method can be used as a first step to evaluate whether a particular condition results in an alteration of protein aggregate formation levels.

Hydrolytic Activity of Esterase-Antibody Complexes Retained Within Gel Capsules After Complex Isolation

Delipidation in biological samples is important for some diagnostic tests and protein analyses. Lipids in the samples can be hydrolyzed by native esterases (ESs) within gel capsules after ES, and ES-antibody complexes are specifically trapped, extracted, and separated. Acrylamide and agarose gel capsules containing complexes of ES antibody were produced after the complexes were extracted using protein A-immobilized membranes, separated by non-denaturing electrophoresis, and stained by colloidal silver using glucose as a reductant. ES activity of ES-antibody complexes within the gel capsule was significantly higher than that in the complexes with the control antibodies upon isolation, separation, and detection of the complex. In addition, lipids bound to human serum albumin decreased after human plasma was treated with gel capsules containing ES-antibody complexes. We demonstrate that the gel capsule containing ES-antibody complexes can be successfully isolated using techniques described in this study. Furthermore, delipidation of human plasma is obtained by incubation with the gel capsule. These results indicate that surplus materials such as lipids in biological samples can be removed or reduced by gel capsule containing enzymes.

Histopathology

The detection of fungal elements and their characterization in patient specimens provides fundamental information. On histological sections fungi are most frequently seen on skin or mucosal surfaces or as mycotic thrombi or emboli that can occlude both arteries and veins in surgical specimen from immunocompromised patients or tissues obtained from autopsies. Microbial culture continues to be the central method for diagnosing fungal infection but is complemented by histomorphology using specific stains capable of identifying previously unsuspected fungal infections or for evaluating tissue invasion. These stains employ oxidizing reagents to create aldehyde binding sites on polysaccharides (1,2-glycol groups) of fungal cell walls for either Schiff's reagent or Silver ions. Gomori methenamine silver (GMS) and Periodic acid-Schiff (PAS) or their modifications are the most commonly used for tissue sections and in cytology specimens.

Staining and Transfer Techniques for SDS-PAGE Gels to Minimize Oil-in-Water Emulsion Adjuvant Interference

Adjuvants in modern vaccines boost and shape immune responses and allow for antigen dose-sparing. Analysis of protein antigens in the presence of adjuvants can prove challenging, especially if the adjuvant interferes with visualization of the protein band on an SDS-PAGE gel. In this chapter, a variety of different techniques are presented to mitigate the interference of a nanoemulsion adjuvant, GLA-SE, with different recombinant proteins of varying molecular weight by addressing sample preparation and staining methods.

Mass Spectrometry-Based Biomarker Discovery

The discovery of candidate biomarkers within the entire proteome is one of the most important and challenging goals in proteomic research. Mass spectrometry-based proteomics is a modern and promising technology for semiquantitative and qualitative assessment of proteins, enabling protein sequencing and identification with exquisite accuracy and sensitivity. For mass spectrometry analysis, protein extractions from tissues or body fluids and subsequent protein fractionation represent an important and unavoidable step in the workflow for biomarker discovery. Following extraction of proteins, the protein mixture must be digested, reduced, alkylated, and cleaned up prior to mass spectrometry. The aim of our chapter is to provide comprehensible and practical lab procedures for sample digestion, protein fractionation, and subsequent mass spectrometry analysis.